When changing the frequency of the sinusoidal profile, you may notice noise and resonance at different frequency values. There are several possible causes.
EMI - Make sure all your cables are properly shielded and ground the shields. Make sure the analog input wiring is twisted-pair and shielded. Follow the recommendations in the articles on this site: Grounding and Shielding Landing Page (Prevent Noise Issues) | Kollmorgen
Tuning - The resonance could be due to improper tuning. If the velocity loop is in the drive and the position loop is in the controller, you must tune both to make sure they are balanced. You can use the Performance Servo Tuner in Workbench to autotune the velocity loop in the drive, but you will likely need to make manual adjustments to the velocity gains while tuning the position loop in the controller.
Cables - The motor power and feedback cables for the linear motor and linear encoder will move as the motor moves. Make sure to follow proper bend radius limitations. If you are powering the drive with 400V/480VAC, putting the motor power cable and the feedback cable together in a cable track may not be ideal. The cables should be separated by several inches at least. Also, make sure that the cables you are using are rated for flexing. If the cables are not flex rated, as the cables flex/bend, the shield moves and can open up allowing EMI.
Encoder resolution - The 2.5 micron AquadB encoder is relatively low resolution. 2.5 microns = 12800 lines per 32mm (1 pole-pair) = 51200 counts (post quad). That is not the worst resolution, but it is relatively low compared to very high resolution encoders. The resolution affects the overall performance.
EEO - If you are using an Emulated Encoder Output (EEO), the EEO resolution needs to be set as high as possible without exceeding the maximum frequency limit. A low EEO resolution is the same as using a linear encoder with a low resolution. It will give poor performance and make it difficult to tune.